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Minor tweaks to SubstructLibrary (#3564)

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* - added some missing const keywords
- added an addFingerprint overload to allow passing pointers
- added a test

* changes in response to review

* removed print

* added missing shared_ptr declaration

* added PatternNumBitsHolder serialization

* - merged with upstream changes and resolved conflicts
- got rid of PatternNumBitsHolder and leveraged the serialization version to get the PatternHolder to be backwards-compatible

* built substructLibV1.pkl with an older version of boost

* reverted serialization version to 1
only write numBits if != 2048 and only read numBits if it exists in the archive

* bogus commit just to trigger a rebuild
This commit is contained in:
Paolo Tosco
2020-12-10 01:42:38 +01:00
committed by GitHub
parent e7e17adc4e
commit 8030c36e5b
7 changed files with 195 additions and 43 deletions
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96
Code/GraphMol/SubstructLibrary/substructLibraryTest.cpp
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@@ -113,7 +113,7 @@ void test1() {
std::vector<SubstructLibrary*> libs;
libs.push_back(&ssslib);
#ifdef RDK_USE_BOOST_SERIALIZATION
#ifdef RDK_USE_BOOST_SERIALIZATION
std::string pickle = ssslib.Serialize();
SubstructLibrary serialized;
serialized.initFromString(pickle);
@@ -188,7 +188,7 @@ void test2() {
std::vector<SubstructLibrary*> libs;
libs.push_back(&ssslib);
#ifdef RDK_USE_BOOST_SERIALIZATION
#ifdef RDK_USE_BOOST_SERIALIZATION
std::string pickle = ssslib.Serialize();
SubstructLibrary serialized;
serialized.initFromString(pickle);
@@ -239,7 +239,7 @@ void test3() {
std::vector<SubstructLibrary*> libs;
libs.push_back(&ssslib);
#ifdef RDK_USE_BOOST_SERIALIZATION
#ifdef RDK_USE_BOOST_SERIALIZATION
std::string pickle = ssslib.Serialize();
SubstructLibrary serialized;
serialized.initFromString(pickle);
@@ -289,7 +289,7 @@ void test4() {
std::vector<SubstructLibrary*> libs;
libs.push_back(&ssslib);
#ifdef RDK_USE_BOOST_SERIALIZATION
#ifdef RDK_USE_BOOST_SERIALIZATION
std::string pickle = ssslib.Serialize();
SubstructLibrary serialized;
serialized.initFromString(pickle);
@@ -564,6 +564,93 @@ void testMaxResultsAllSameNumThreads() {
}
}
void testPatternHolder() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " testPatternHolder" << std::endl;
std::string fName = getenv("RDBASE");
fName += "/Data/NCI/first_5K.smi";
SmilesMolSupplier suppl(fName, "\t", 0, 1, false);
boost::shared_ptr<CachedTrustedSmilesMolHolder> mols1(
new CachedTrustedSmilesMolHolder());
boost::shared_ptr<PatternHolder> fps1(new PatternHolder());
SubstructLibrary ssslib1(mols1, fps1);
boost::shared_ptr<CachedTrustedSmilesMolHolder> mols2(
new CachedTrustedSmilesMolHolder());
boost::shared_ptr<PatternHolder> fps2(new PatternHolder());
SubstructLibrary ssslib2(mols2, fps2);
boost::logging::disable_logs("rdApp.error");
for (unsigned int i = 0; i < 1000; i += 10) {
ROMol *mol = nullptr;
try {
mol = suppl[i];
} catch (...) {
continue;
}
if (!mol) {
continue;
}
mols1->addSmiles(MolToSmiles(*mol));
fps1->addFingerprint(fps1->makeFingerprint(*mol));
ssslib2.addMol(*mol);
delete mol;
}
boost::logging::enable_logs("rdApp.error");
ROMOL_SPTR query(SmartsToMol("N"));
TEST_ASSERT(query);
{
auto matches1 = ssslib1.getMatches(*query);
std::sort(matches1.begin(), matches1.end());
auto matches2 = ssslib2.getMatches(*query);
std::sort(matches2.begin(), matches2.end());
TEST_ASSERT(matches1.size() == matches2.size());
for (size_t i = 0; i < matches1.size(); ++i) {
TEST_ASSERT(matches1.at(i) == matches2.at(i));
}
}
#ifdef RDK_USE_BOOST_SERIALIZATION
std::string pickle = ssslib1.Serialize();
SubstructLibrary serialized;
serialized.initFromString(pickle);
TEST_ASSERT(serialized.size() == ssslib1.size());
SubstructLibrary serializedLegacy;
std::string pklName = getenv("RDBASE");
TEST_ASSERT(!pklName.empty());
pklName += "/Code/GraphMol/test_data/substructLibV1.pkl";
std::ifstream pickle_istream(pklName.c_str(), std::ios_base::binary);
serializedLegacy.initFromStream(pickle_istream);
pickle_istream.close();
TEST_ASSERT(serializedLegacy.size() == serialized.size());
{
auto matches1 = serializedLegacy.getMatches(*query);
std::sort(matches1.begin(), matches1.end());
auto matches2 = serialized.getMatches(*query);
std::sort(matches2.begin(), matches2.end());
TEST_ASSERT(matches1.size() == matches2.size());
for (size_t i = 0; i < matches1.size(); ++i) {
TEST_ASSERT(matches1.at(i) == matches2.at(i));
}
}
for (size_t i = 0; i < 2; ++i) {
auto serialized_pattern_holder =
dynamic_cast<PatternHolder *>(serialized.getFpHolder().get());
TEST_ASSERT(serialized_pattern_holder);
auto orig_pattern_holder =
dynamic_cast<PatternHolder *>(ssslib1.getFpHolder().get());
TEST_ASSERT(orig_pattern_holder);
TEST_ASSERT(serialized_pattern_holder->getNumBits() ==
orig_pattern_holder->getNumBits());
if (i) {
break;
}
orig_pattern_holder->getNumBits() = 1024;
pickle = ssslib1.Serialize();
serialized.initFromString(pickle);
}
#endif
}
int main() {
RDLog::InitLogs();
#if 1
@@ -574,6 +661,7 @@ int main() {
docTest();
ringTest();
testAddPatterns();
testPatternHolder();
#ifdef RDK_TEST_MULTITHREADED
testMaxResultsNumThreads();
testMaxResultsAllSameNumThreads();